scholarly journals The Living Atlases community in action: general introduction

2018 ◽  
Vol 2 ◽  
pp. e25487
Author(s):  
Marie-Elise Lecoq ◽  
Anne-Sophie Archambeau ◽  
Fabien Cavière ◽  
David Martin ◽  
Nick dos Remedios
Keyword(s):  
Training Session ◽  
Technical Documentation ◽  
Community Members ◽  
General Introduction ◽  
Global Biodiversity Information Facility ◽  
Capacity Enhancement ◽  
Support Programme ◽  
Work Done ◽  
Biodiversity Information ◽  
New Infrastructure

Atlas of Living Australia (ALA) (https://www.ala.org.au/) is the Global Biodiversity Information Facility (GBIF) node of Australia. In 2010, they launched an open and free platform for sharing and exploring biodiversity data. Thanks to this new infrastructure, they have been able to drastically increase the number of occurrences published through the GBIF.org . In order to help other GBIF nodes or institutions, they made all of their modules publicly available for reuse and customization through GitHub (https://github.com/AtlasOfLivingAustralia). Since 2013, the community created by developers interested by ALA tools, organized, with the help of GBIF, 8 technical workshops around the world. These workshops helped the launch of at least 13 data portals. The last training session, funded through the GBIF Capacity Enhancement Support Programme (https://www.gbif.org/programme/82219/capacity-enhancement-support-programme), was been attended by 23 participants from 19 countries on 6 continents. Moreover, on the new GBIF website, a section has been dedicated to this programme (https://www.gbif.org/programme/82953/living-atlases), the Living Atlases community official website has been launched in 2017 (https://living-atlases.gbif.org) and the technical documentation has been improved and translated in several languages. All of these achievements would not have been possible without a huge effort from the ALA developer community. After a brief introduction of the Living Atlases community, we will present you the work done by ALA to simplify the process of getting a living atlas up and running. We will also show you how ALA developers managed to help the community members to create their own version by performing simple HTML/CSS customizations.

scholarly journals The Living Atlases community in action: the GBIF Benin data portal

2018 ◽  
Vol 2 ◽  
pp. e25488
Author(s):  
Anne-Sophie Archambeau ◽  
Fabien Cavière ◽  
Kourouma Koura ◽  
Marie-Elise Lecoq ◽  
Sophie Pamerlon ◽  
...  
Keyword(s):  
African Country ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Capacity Enhancement ◽  
Support Programme ◽  
Data Portal ◽  
Global Biodiversity ◽  
The University ◽  
Biodiversity Information ◽  
Occurrence Records

Atlas of Living Australia (ALA) (https://www.ala.org.au/) is the Global Biodiversity Information Facility (GBIF) node of Australia. They developed an open and free platform for sharing and exploring biodiversity data. All the modules are publicly available for reuse and customization on their GitHub account (https://github.com/AtlasOfLivingAustralia). GBIF Benin, hosted at the University of Abomey-Calavi, has published more than 338 000 occurrence records from 87 datasets and 2 checklists. Through the GBIF Capacity Enhancement Support Programme (https://www.gbif.org/programme/82219/capacity-enhancement-support-programme), GBIF Benin, with the help of GBIF France, is in the process of deploying the Beninese data portal using the GBIF France back-end architecture. GBIF Benin is the first African country to implement this module of the ALA infrastructure. In this presentation, we will show you an overview of the registry and the occurrence search engine using the Beninese data portal. We will begin with the administration interface and how to manage metadata, then we will continue with the user interface of the registry and how you can find Beninese occurrences through the hub.

scholarly journals GBIF Benin's Data Portal

2018 ◽  
Vol 2 ◽  
pp. e25890
Author(s):  
Marie-Elise Lecoq ◽  
Anne-Sophie Archambeau ◽  
Fabien Cavière ◽  
Kourouma Koura ◽  
Sophie Pamerlon ◽  
...  
Keyword(s):  
Information Technologies ◽  
Geographic Area ◽  
Transfer Of Knowledge ◽  
Global Biodiversity Information Facility ◽  
Capacity Enhancement ◽  
Support Programme ◽  
Data Portal ◽  
The University ◽  
Different Levels ◽  
Biodiversity Information

GBIF Benin, hosted at the University of Abomey-Calavi, has published more than 338,000 occurrence records in 87 datasets and checklists. It has been a Global Biodiversity Information Facility (GBIF) node since 2004 and is a leader in several projects from the Biodiversity Information for Development (BID) programme. GBIF facilitates collaboration between nodes at different levels through its Capacity Enhancement Support Programme (CESP) [https://www.gbif.org/programme/82219/capacity-enhancement-support-programme]. One of the actions included in the CESP guidelines is called ‘Mentoring activities’. Its main goal is the transfer of knowledge between partners such as information, technologies, experience, and best practices. Sharing architecture and development is the key solution to solve some technical challenges or impediments (hosting, staff turnover, etc.) that GBIF nodes could face. The Atlas of Living Australia (ALA) team developed a functionality called ‘data hub’. It gives the possibility to create a standalone website with a dedicated occurrence search engine that seeks among a range of data (e.g. specific genus, geographic area). In 2017, GBIF Benin and GBIF France wanted to strengthen their partnership and started a CESP project. One of the core objectives of this project is the creation of the Atlas of Living Benin using ALA modules. GBIF France developers, with the help of the GBIF Benin team, are in the process of configuring a data hub that will give access to Beninese data only, while at the same time Atlas of Living France will give access to French data only. Both data portals will use the same back end, therefore the same databases. Benin is the first African GBIF node to implement this kind of infrastructure. On this poster, we will present the Atlas of Living Benin specific architecture and how we have managed to distinguish data coming from Benin and coming from France.

scholarly journals Three Portals, One Infrastructure: How to manage information with ALA tools

2019 ◽  
Vol 3 ◽  
Author(s):  
Fabien Cavière ◽  
Anne-Sophie Archambeau ◽  
Raoufou Radji ◽  
Christian Ahadji ◽  
Sophie Pamerlon
Keyword(s):  
Information Technologies ◽  
Its Region ◽  
Geographic Area ◽  
Transfer Of Knowledge ◽  
Global Biodiversity Information Facility ◽  
Support Programme ◽  
Management Procedure ◽  
The Creation ◽  
The University ◽  
Biodiversity Information

GBIF Togo, hosted at the University of Lomé, has published more than 62,200 occurrence records from 37 datasets and checklists. As a node participant of Global Biodiversity Information Facility (GBIF) since 2011, it has participated actively in several projects including the Biodiversity Information for Development (BID) programme. GBIF facilitates collaboration between nodes at different levels through its Capacity Enhancement Support Programme (CESP). One of the actions included in the CESP guidelines is called ‘Mentoring activities’. Its main goal is the transfer of knowledge between partners, such as information, technologies, experience, and best practices. Sharing architecture and development is the key solution to solving some the technical challenges and impediments (e.g. hosting, staff turnover, etc.) that GBIF nodes occasionally face. The Atlas of Living Australia (ALA) team have developed a feature called ‘data hub’, which allows the creation of a standalone website with a dedicated occurrence search engine that supports data discovery (e.g. specific genus, geographic area) published by particular GBIF nodes. In 2017, a CESP project between the GBIF Benin and the GBIF France led to the creation of a new portal: Atlas of Living Beninises. This portal shared the same back-end database as the Atlas of Living France portal, while at the same time, each portal displayed and managed information relevant only to its region. In 2018, another CESP project between GBIF France and GBIF Togo shared the same goal as the previous one: implement a new Atlas of Living Australia portal for Togo. This goal will be fulfilled using a similar implementation as the previous project: a shared back-end and different front-end. Togo will be the second African GBIF node to implement this kind of infrastructure. This poster will highlight the architecture specific to the Atlas of Living Togo, and present the management procedure that distinguishes data coming from the three different countries.

scholarly journals The Living Atlases Community: Communication and documentation

2020 ◽  
Vol 4 ◽  
Author(s):  
Marie-Elise Lecoq ◽  
Vicente Ruiz Jurado
Keyword(s):  
End Users ◽  
The Internet ◽  
Technical Documentation ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Network Nodes ◽  
Twitter Account ◽  
Global Biodiversity ◽  
One Year ◽  
Biodiversity Information

Managers and developers from organizations within the Global Biodiversity Information Facility (GBIF) network nodes using the Atlas of Living Australia (ALA) modules have created the Living Atlases (LA) community. Since the beginning, two of our priorities have been the technical guides and communication inside and outside our network. A community can not be sustainable without useful technical documentation, as members must work by themselves as much as possible. Without communication, a community cannot grow either. More than one year ago, the Living Atlases community hired a technical coordinator, Vicente J. Ruiz Jurado. With the help of other participants, he greatly improved our technical documentation with the Living Atlas Quick Start Guide and increased communication with remote support sessions. The helpdesk, through the use of the LA Slack channel, has been improved as well. We have also increased our visibility on the Internet with our website and our Twitter account. Over the last few years, we have focused our work on end-users, with dedicated workshops, including exercises made by participants for their users and two videos showing how a Living Atlas works (How to search and download biodiversity data in an Atlas and How to use regions/spatial module in an Atlas).

scholarly journals Furthering Genomic Research Infrastructures: The Global Genome Biodiversity Network

2019 ◽  
Vol 3 ◽  
Author(s):  
Katharine Barker ◽  
Jonas Astrin ◽  
Gabriele Droege ◽  
Jonathan Coddington ◽  
Ole Seberg
Keyword(s):  
Natural History ◽  
Best Practices ◽  
Genomic Research ◽  
Benefit Sharing ◽  
Global Biodiversity Information Facility ◽  
Access And Benefit Sharing ◽  
Culture Collections ◽  
Data Standard ◽  
Research Infrastructures ◽  
Biodiversity Information

Most successful research programs depend on easily accessible and standardized research infrastructures. Until recently, access to tissue or DNA samples with standardized metadata and of a sufficiently high quality, has been a major bottleneck for genomic research. The Global Geonome Biodiversity Network (GGBN) fills this critical gap by offering standardized, legal access to samples. Presently, GGBN’s core activity is enabling access to searchable DNA and tissue collections across natural history museums and botanic gardens. Activities are gradually being expanded to encompass all kinds of biodiversity biobanks such as culture collections, zoological gardens, aquaria, arboreta, and environmental biobanks. Broadly speaking, these collections all provide long-term storage and standardized public access to samples useful for molecular research. GGBN facilitates sample search and discovery for its distributed member collections through a single entry point. It stores standardized information on mostly geo-referenced, vouchered samples, their physical location, availability, quality, and the necessary legal information on over 50,000 species of Earth’s biodiversity, from unicellular to multicellular organisms. The GGBN Data Portal and the GGBN Data Standard are complementary to existing infrastructures such as the Global Biodiversity Information Facility (GBIF) and International Nucleotide Sequence Database (INSDC). Today, many well-known open-source collection management databases such as Arctos, Specify, and Symbiota, are implementing the GGBN data standard. GGBN continues to increase its collections strategically, based on the needs of the research community, adding over 1.3 million online records in 2018 alone, and today two million sample data are available through GGBN. Together with Consortium of European Taxonomic Facilities (CETAF), Society for the Preservation of Natural History Collections (SPNHC), Biodiversity Information Standards (TDWG), and Synthesis of Systematic Resources (SYNTHESYS+), GGBN provides best practices for biorepositories on meeting the requirements of the Nagoya Protocol on Access and Benefit Sharing (ABS). By collaboration with the Biodiversity Heritage Library (BHL), GGBN is exploring options for tagging publications that reference GGBN collections and associated specimens, made searchable through GGBN’s document library. Through its collaborative efforts, standards, and best practices GGBN aims at facilitating trust and transparency in the use of genetic resources.

scholarly journals The InBIO Barcoding Initiative Database: DNA barcodes of Portuguese Diptera 01

2020 ◽  
Vol 8 ◽  
Author(s):  
Sonia Ferreira ◽  
Rui Andrade ◽  
Ana Gonçalves ◽  
Pedro Sousa ◽  
Joana Paupério ◽  
...  
Keyword(s):  
Species Level ◽  
Distribution Data ◽  
Dna Barcodes ◽  
Online Database ◽  
Global Biodiversity Information Facility ◽  
Life Data ◽  
Tagus River ◽  
Global Biodiversity ◽  
Biodiversity Information ◽  
Dipteran Species

The InBIO Barcoding Initiative (IBI) Diptera 01 dataset contains records of 203 specimens of Diptera. All specimens have been morphologically identified to species level, and belong to 154 species in total. The species represented in this dataset correspond to about 10% of continental Portugal dipteran species diversity. All specimens were collected north of the Tagus river in Portugal. Sampling took place from 2014 to 2018, and specimens are deposited in the IBI collection at CIBIO, Research Center in Biodiversity and Genetic Resources. This dataset contributes to the knowledge on the DNA barcodes and distribution of 154 species of Diptera from Portugal and is the first of the planned IBI database public releases, which will make available genetic and distribution data for a series of taxa. All specimens have their DNA barcodes made publicly available in the Barcode of Life Data System (BOLD) online database and the distribution dataset can be freely accessed through the Global Biodiversity Information Facility (GBIF).

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